Two commercial shrimp species (Penaeus californiensis and P. stylirostris) were sampled along the Gulf of California and crude extracts were assayed electrophoretically to assess allozyme variation and population genetic structure. Penaeus californiensis, a more oceanic species, displayed a 12.5% polymorphism (P95) and a 0.023-0.037 expected heterozygosity (He) in three sampled populations, whereas P. stylirostris, a more coastal species, showed a north-south clinelike pattern in its genetic variability parameters: P95 from 15.63% to 31.25% and He from 0.038 to 0.086. Differences between species in levels of genetic variation and genotype distribution may be related to differences in habitat during important life cycles stages which reflect the remarkable changes of environmental conditions of coastal lagoons in the Gulf of California. Penaeus stylirostris subpopulations appeared more structured (Fst = 0.372) than those of P. californiensis (Fst = 0.182). A number of private alleles and alternation of the most common allele in several loci account for the outstanding high results of both species. Nei's genetic similarities were computed within species (P. californiensis subpopulations, I =0.988-0.997; P. stylirostris subpopulations, I = 0.929-0.954) and between species (P. californiensis x P. stylirostris, I = 0.674). A dendrogram generated from Nei's genetic similarities segregated the upper Gulf populations of both species from the other two populations (middle Gulf and mouth of the Gulf). This segregation may be the result of the "Island Barrier" hypothesized as segregating other decapods inhabiting the Gulf of California.